[ccp4bb] Please attend a workshop on Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

Driven by recent advances in this field we will hold a workshop to discuss it. The workshop will be on Monday, May 15, 2017 at Brookhaven Nat'l Laboratory, and will be affiliated with the 2017 Users' Meeting for NSLS-II and the Center for Functional Nanomaterials. The current draft agenda is

Re: [ccp4bb] Ramachandran statistics and referee responsibility

I'd expect imposing Ramachandran restraints to lower the Rfree or at least the gap between R and Free, otherwise I would not do it. If there were genuine Ramachandran outliers, the restrained model might not have these included, while these outliers could potentially be very interesting. Of

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

I must also credit Robbie with the easiest (most elegant?) solution to my question. You run 0 cycles of refmac with the mixed B factor model. Thanks all for your inputs. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

Normally, these days at least, a model that is result of TLS refinement contains total B factor in ANISOU records and its TLS component in TLS records (REMARK3), with Btotal = Btls+Bresidual. If TLS matrices are available, it's trivial to calculate Btls from TLS matrices in REMARK3 and subtract

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

Hi Eleanor, This is covered in PDB_REDO: we figure out whether the B-factors are totals or residuals. Wouter Touw has made the BDB (http://www.cmbi.ru.nl/bdb/) a databank in which all B-factors are represented as the isotropic component of the total B-factor. This is quite useful if you want

[ccp4bb] A NIH funded postdoctoral fellow position for CryoEM and/or protein crystallography

A NIH funded postdoctoral fellow position for CryoEM and/or protein crystallography is available immediately in Dr. Xu’s laboratory at the Department of Molecular and Structural Biochemistry at North Carolina State University. Research in Xu lab focuses on structural elucidation of protein

[ccp4bb] PhD UCL/National Institute of Biological Standards and Control (NIBSC)

The very excellent Dr Clive Metcalfe (an ex-post-doc with me) of NIBSC has a PhD project with Prof Paul Dalby at UCL looking at disulphide bond reduction in monoclonal antibodies. If you have a good student who might be interested please point them to https://www.prism.ucl.ac.uk/#!/?project=205

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

Actually I think it is pretty dangerous to trust the TLS stuff in the PDB header - there is a muddle between B_residual and B_merged and no adequate description in the header. Unless you are planning on doing many many repeats I would re-refine before checking the map... eleanor On 8 March 2017

Re: [ccp4bb] Ramachandran statistics and referee responsibility

Hi Evette, (1) best practices in refining against lower resolution data (~4 angstrom) > to achieve the best model, > obtain a model that fits data best under requirement that it has zero geometry violations (Ramachandran, Cbeta deviations, rotamers, CABLAM, etc..). Note, a geometry outlier

[ccp4bb] Ramachandran statistics and referee responsibility

Dear all, I have two questions. I would like to find out the community consensus of (1) best practices in refining against lower resolution data (~4 angstrom) to achieve the best model, and also (2) what manuscript referees should ask for in this regard. One might encounter a hypothetical

[ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

It would be nice to be able to run zero cycles of refmac to get a map etc direct from a PDB file. However due the PDB requiring the TLS component of B factor to be included this does not work. Is there software to remove the TLS component so a zero cycle of refmac can be run. Best wishes

Re: [ccp4bb] Removing TLS component of B factor of deposited PDB files to input to refmac

TLSANL? Eleanor On 8 March 2017 at 14:08, Nicholas Keep wrote: > It would be nice to be able to run zero cycles of refmac to get a map etc > direct from a PDB file. > > However due the PDB requiring the TLS component of B factor to be included > this does not work.